anndataR

anndataR enables native manipulation and analysis of single-cell transcriptomics data in R by providing interoperability with the Python AnnData ecosystem.

Key Features:

• H5AD File I/O: Natively reads and writes HDF5-backed AnnData (H5AD) files in R with guaranteed compatibility between Python-written and R-written files.
• Zarr File Support: Works with backed zarr files for single-cell data storage and access.
• Direct Slot Access: Allows direct access to AnnData slots including X, obs, and var without full data loading.
• Object Conversion: Converts AnnData objects to and from SingleCellExperiment and Seurat objects.
• Native R AnnData Object: Supports working with R AnnData objects directly within the R environment.

Scientific Applications:

• Cross-Language Single-Cell Analysis: Facilitates access to scverse ecosystem datasets from R, enabling users to leverage the strengths of both programming languages.
• Large-Scale Single-Cell Transcriptomics: Enables manipulation and analysis of large single-cell transcriptomics datasets stored in H5AD format without requiring Python.
• Workflow Integration: Integrates Python-generated single-cell datasets into R-based analytical workflows using SingleCellExperiment or Seurat.

Methodology:

Rigorous testing ensures compatibility between Python-written and R-written H5AD files for long-term interoperability.